feat: allow 'not_specified' classifications to overlap in score calibration ranges

Author: bencap

src/mavedb/view_models/score_calibration.py

@@ -17,14 +17,14 @@
 )
 from mavedb.lib.validation.utilities import inf_or_float
 from mavedb.view_models import record_type_validator, set_record_type
-from mavedb.view_models.base.base import BaseModel
 from mavedb.view_models.acmg_classification import (
+    ACMGClassification,
     ACMGClassificationBase,
     ACMGClassificationCreate,
     ACMGClassificationModify,
     SavedACMGClassification,
-    ACMGClassification,
 )
+from mavedb.view_models.base.base import BaseModel
 from mavedb.view_models.publication_identifier import (
     PublicationIdentifier,
     PublicationIdentifierBase,
@@ -33,7 +33,6 @@
 )
 from mavedb.view_models.user import SavedUser, User
 
-
 ### Functional range models
 
 
@@ -197,6 +196,10 @@ def ranges_do_not_overlap(
         """Ensure that no two functional ranges overlap (respecting inclusivity)."""
 
         def test_overlap(range_test: FunctionalRangeBase, range_check: FunctionalRangeBase) -> bool:
+            # Allow 'not_specified' classifications to overlap with anything.
+            if range_test.classification == "not_specified" or range_check.classification == "not_specified":
+                return False
+
             if min(inf_or_float(range_test.range[0], True), inf_or_float(range_check.range[0], True)) == inf_or_float(
                 range_test.range[0], True
             ):
@@ -223,7 +226,7 @@ def test_overlap(range_test: FunctionalRangeBase, range_check: FunctionalRangeBa
             for b in list(field_value)[i + 1 :]:
                 if test_overlap(a, b):
                     raise ValidationError(
-                        f"Score ranges may not overlap; `{a.label}` ({a.range}) overlaps with `{b.label}` ({b.range}).",
+                        f"Classified score ranges may not overlap; `{a.label}` ({a.range}) overlaps with `{b.label}` ({b.range}). To allow overlap, set one or both classifications to 'not_specified'.",
                         custom_loc=["body", i, "range"],
                     )
         return field_value

tests/view_models/test_score_calibration.py

@@ -11,21 +11,19 @@
     ScoreCalibrationCreate,
     ScoreCalibrationWithScoreSetUrn,
 )
-
 from tests.helpers.constants import (
-    TEST_FUNCTIONAL_RANGE_NORMAL,
+    TEST_BRNICH_SCORE_CALIBRATION,
     TEST_FUNCTIONAL_RANGE_ABNORMAL,
-    TEST_FUNCTIONAL_RANGE_NOT_SPECIFIED,
-    TEST_FUNCTIONAL_RANGE_INCLUDING_POSITIVE_INFINITY,
     TEST_FUNCTIONAL_RANGE_INCLUDING_NEGATIVE_INFINITY,
-    TEST_BRNICH_SCORE_CALIBRATION,
+    TEST_FUNCTIONAL_RANGE_INCLUDING_POSITIVE_INFINITY,
+    TEST_FUNCTIONAL_RANGE_NORMAL,
+    TEST_FUNCTIONAL_RANGE_NOT_SPECIFIED,
     TEST_PATHOGENICITY_SCORE_CALIBRATION,
     TEST_SAVED_BRNICH_SCORE_CALIBRATION,
     TEST_SAVED_PATHOGENICITY_SCORE_CALIBRATION,
 )
 from tests.helpers.util.common import dummy_attributed_object_from_dict
 
-
 ##############################################################################
 # Tests for FunctionalRange view models
 ##############################################################################
@@ -260,22 +258,43 @@ def test_can_create_valid_score_calibration_without_functional_ranges(valid_cali
         assert sc.calibration_metadata is None
 
 
-def test_cannot_create_score_calibration_when_ranges_overlap():
+def test_cannot_create_score_calibration_when_classification_ranges_overlap():
     invalid_data = deepcopy(TEST_BRNICH_SCORE_CALIBRATION)
     # Make the first two ranges overlap
     invalid_data["functional_ranges"][0]["range"] = [1.0, 3.0]
     invalid_data["functional_ranges"][1]["range"] = [2.0, 4.0]
-    with pytest.raises(ValidationError, match="Score ranges may not overlap; `"):
+    with pytest.raises(ValidationError, match="Classified score ranges may not overlap; `"):
         ScoreCalibrationCreate.model_validate(invalid_data)
 
 
+def test_can_create_score_calibration_when_unclassified_ranges_overlap_with_classified_ranges():
+    valid_data = deepcopy(TEST_BRNICH_SCORE_CALIBRATION)
+    # Make the first two ranges overlap, one being 'not_specified'
+    valid_data["functional_ranges"][0]["range"] = [1.5, 3.0]
+    valid_data["functional_ranges"][1]["range"] = [2.0, 4.0]
+    valid_data["functional_ranges"][0]["classification"] = "not_specified"
+    sc = ScoreCalibrationCreate.model_validate(valid_data)
+    assert len(sc.functional_ranges) == len(valid_data["functional_ranges"])
+
+
+def test_can_create_score_calibration_when_unclassified_ranges_overlap_with_each_other():
+    valid_data = deepcopy(TEST_BRNICH_SCORE_CALIBRATION)
+    # Make the first two ranges overlap, both being 'not_specified'
+    valid_data["functional_ranges"][0]["range"] = [1.5, 3.0]
+    valid_data["functional_ranges"][1]["range"] = [2.0, 4.0]
+    valid_data["functional_ranges"][0]["classification"] = "not_specified"
+    valid_data["functional_ranges"][1]["classification"] = "not_specified"
+    sc = ScoreCalibrationCreate.model_validate(valid_data)
+    assert len(sc.functional_ranges) == len(valid_data["functional_ranges"])
+
+
 def test_cannot_create_score_calibration_when_ranges_touch_with_inclusive_ranges():
     invalid_data = deepcopy(TEST_BRNICH_SCORE_CALIBRATION)
     # Make the first two ranges touch
     invalid_data["functional_ranges"][0]["range"] = [1.0, 2.0]
     invalid_data["functional_ranges"][1]["range"] = [2.0, 4.0]
     invalid_data["functional_ranges"][0]["inclusive_upper_bound"] = True
-    with pytest.raises(ValidationError, match="Score ranges may not overlap; `"):
+    with pytest.raises(ValidationError, match="Classified score ranges may not overlap; `"):
         ScoreCalibrationCreate.model_validate(invalid_data)